The 3.9 has been pretty standard forever. It is basically a 318 minus 2 cylinders, except because of the lost 2 cylinders it wasn't near as smooth. This is exaggerated even more with the manual and at low rpms. The manual I think is a NV-3500, pretty standard truck transmission with a low first gear. It should get better mileage then the 318 but most people didn't see much better. The 4.7 of a few years later was much better for economy but it's not the most reliable thing around.
here is the most info you can find about anything from Chrysler, at Allpar.com
Dodge Dakota, 1997-2004 baby Ram pickup trucks
and for the motor
http://www.allpar.com/mopar/39.html